Molecular epidemiology of circulating non-virulent and re-emerged virulent infectious salmon anaemia virus (ISAV) in the Faroe lslands

The virulent infectious salmon anaemia virus, designated ISAV-HPR-deleted, is the cuasative agent of a systemic and lethal disease, infectious salmon anaemia (ISA), of farmed Atlantic salmon (Salmo salar L). ISA disease epidemics have raged most major Atlantic salmon producing countries and lack of national management strategies on the prevention and control of ISA played a major role in the devastating consequences of the ISA epidemics. In the Faroe Islands, the ISA epidemic 2000 - 2005 resulted in an almost total collapse of the farming industry. Based on current knowledge on ISA most countries have implemented national management strategies. However, knowledge on ISA virus (ISAV) functional characteristics, aetiology, epidemiology and pathogenesis is incomplete, including the association between non virulent and virulent ISAV variants. In 2014, the first ISA outbreak in the Faroe Islands since the epidemic was ancountered. In this study we aimed to:

1. Identify potential virulence markers by whole genome sequencing (WGS) of various virulent and non-virulent ISAV variants.
2. Identify the origin and spread of the non-virulent ISAV-HPR0 in the three compartments i.e. in brood fish, freshwater smolt farms and marine grow out sites.
3. Determine if one of the ISAV-HPR0 variants circulating in Faroese aquaculture was a progenitor to the virulent ISAV variant identified in 2014 at the marine site.
4. Determine the virulence of the new HPR-deleted by in-vitro immersion challenge.
5. Determine tissue tropism of ISAV-HPR0.

In the present study we demonstrate that the non-virulent subtype of ISAV (ISAV-HPR0) is endemic in all three production stages of Atlantic salmon including brood fish, freshwater hatcheries/smolt farms and at marine grow-out sites where it causes a sesonal and non-clinical transient infection (Christiansen et al., 2011 and 2021). Previous work has shown that the virulent ISAV-HPR-deleted variant causes a systemic infection targeting endothelial cells. Here we show that ISAV-HPR0 has a different tissue tropism and causes an active infection and replication in the epithelial cells of the gills and skin of Atlantic salmon (Aamelfot et al., 2015, Petersen et al., 2023).
The non-virulent ISAV-HPR0 has been proposed to be the progenitor and reservoir for all virulent ISAVs and thus represent a potential risk factor for the emegrence of ISA disease. Here, we provide the first field evidence of genetic and functional evolution of ISAV-HPR0 to a low-virulent ISAV-HPRdeleted (Christiansen et al., 2017). In the immersion challenge and statistical modelling of viral replication kinetics we demonstrated that fish infected with low-virulent variants showed lower replication efficiencies and different immune responses than fish infected with high-virulent ISAV variant (McBeath et al., 2014a, 2014b). Taken together, the present work shows that mutations of the F and HE genes are key first steps in the within-host infection dynamics i.e. the functional shift of cell and organ trophisms (Christiansen et al. 2017).
In general, a virus may be transmitted by horizontal or vertical routes, or both. The question whether ISAV is vertically transmitted has been, and still is, controversial. Here we demonstrate that ISAV-HPR0 is not transmitted vertically from parents to ofspring’s. On the contrary, the geographical clustering of various HPR0 variants emphasizes the importance of horizontal transmission as a driving force of spreading HPR0 within and between the three production stages of Atlantic salmon (Christiansen et al., 2021).